Watersheds in the subtropical Himalayan basins are highly prone to land degradation due to deforestation, landslides, intensive agriculture, population pressure, and overgrazing, in particular, where various fluvial and denudation processes occur. It is important to assess the magnitude of problem and to understand the erosion process under normal conditions, so that effective measures can be implemented. Therefore, the study selected Kalsa watershed from the Lesser Himalayan region, where soil erosion is more prominent. Regarding this issue, to identify the hotspot of soil erosion of the basin, watershed prioritization methods using advanced geographical information system and remote sensing techniques integrated with weighted sum analysis (WSA) and principal component analysis (PCA). In addition, a comparison has been made to evaluate the performance of these models. The study considered sixteen different morphometric parameters, including linear (Rho coefficient, stream frequency, drainage density, length of overland flow, drainage texture, and constant of channel maintenance); landscape (relative relief, relief ratio, basin slope, and ruggedness number); and shape (elongation ratio, form factor, circulatory ratio, and compactness coefficient). Both the method PCA and WSA indicate the same results showing high priority, meaning the outlet watersheds have high priority. The sub-watersheds in the north-eastern part have the lowest priority. The results also show that the length overland flow, relative relief, basin relief ratio and hypsometric integral are the most important indicators. The sub-watersheds prioritize high ranks, medium ranks, and low ranks out of 10 sub-watersheds covering about 45.32%, 27.78% and 26.90% area of the Kalsa River watershed, respectively. This study will help regional planners, farmers, and governments take more detailed decisions to propose efficient soil erosion control measures and conservation priorities of the watershed. The study findings have implications for sustainable land management and conservation goal targets (target 2.3 and 2.4; target 3.9; target 13.1, 13.2 and 13.3; target 15.3 and 15.4), which finally helps to achieve the United Nation’s 2030 Agenda for Sustainable Development.